This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level results and 9 clinical features across 857 patients, 3 significant findings detected with Q value < 0.25.
-
4q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
-
11p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
-
14q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.
Clinical Features |
Time to Death |
AGE | GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | t-test | t-test | Chi-square test | |
4q gain | 0 (0%) | 830 |
0.0247 (1.00) |
0.353 (1.00) |
1 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.435 (1.00) |
0.689 (1.00) |
3.84e-12 (2.46e-09) |
|
11p gain | 0 (0%) | 793 |
0.617 (1.00) |
0.735 (1.00) |
0.504 (1.00) |
0.763 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.4 (1.00) |
0.000337 (0.215) |
|
14q gain | 0 (0%) | 782 |
0.161 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.329 (1.00) |
0.94 (1.00) |
0.142 (1.00) |
0.0333 (1.00) |
7.8e-05 (0.0498) |
|
1p gain | 0 (0%) | 766 |
0.183 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.0202 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.719 (1.00) |
0.358 (1.00) |
|
1q gain | 0 (0%) | 398 |
0.07 (1.00) |
0.241 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.8 (1.00) |
0.475 (1.00) |
0.573 (1.00) |
0.273 (1.00) |
|
2p gain | 0 (0%) | 809 |
0.784 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.5 (1.00) |
0.777 (1.00) |
0.401 (1.00) |
0.0598 (1.00) |
|
2q gain | 0 (0%) | 832 |
0.97 (1.00) |
0.949 (1.00) |
1 (1.00) |
0.0158 (1.00) |
0.277 (1.00) |
0.337 (1.00) |
0.272 (1.00) |
0.625 (1.00) |
|
3p gain | 0 (0%) | 803 |
0.534 (1.00) |
0.0359 (1.00) |
1 (1.00) |
1 (1.00) |
0.487 (1.00) |
0.4 (1.00) |
0.491 (1.00) |
0.197 (1.00) |
|
3q gain | 0 (0%) | 762 |
0.177 (1.00) |
0.529 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.499 (1.00) |
0.38 (1.00) |
0.174 (1.00) |
0.12 (1.00) |
|
4p gain | 0 (0%) | 828 |
0.0662 (1.00) |
0.477 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.151 (1.00) |
0.489 (1.00) |
0.852 (1.00) |
0.000609 (0.388) |
|
5p gain | 0 (0%) | 695 |
0.173 (1.00) |
0.0573 (1.00) |
0.681 (1.00) |
0.188 (1.00) |
0.467 (1.00) |
0.3 (1.00) |
0.464 (1.00) |
0.75 (1.00) |
|
5q gain | 0 (0%) | 758 |
0.35 (1.00) |
0.0052 (1.00) |
1 (1.00) |
0.267 (1.00) |
0.344 (1.00) |
0.792 (1.00) |
0.866 (1.00) |
0.946 (1.00) |
|
6p gain | 0 (0%) | 764 |
0.831 (1.00) |
0.273 (1.00) |
1 (1.00) |
0.00726 (1.00) |
0.592 (1.00) |
0.9 (1.00) |
0.607 (1.00) |
0.674 (1.00) |
|
6q gain | 0 (0%) | 801 |
0.294 (1.00) |
0.0699 (1.00) |
0.457 (1.00) |
0.522 (1.00) |
0.801 (1.00) |
0.582 (1.00) |
0.962 (1.00) |
0.933 (1.00) |
|
7p gain | 0 (0%) | 705 |
0.859 (1.00) |
0.0902 (1.00) |
0.0113 (1.00) |
0.0127 (1.00) |
0.314 (1.00) |
0.747 (1.00) |
0.416 (1.00) |
0.377 (1.00) |
|
7q gain | 0 (0%) | 747 |
0.496 (1.00) |
0.63 (1.00) |
0.0969 (1.00) |
0.0129 (1.00) |
0.719 (1.00) |
0.323 (1.00) |
0.383 (1.00) |
0.265 (1.00) |
|
8p gain | 0 (0%) | 691 |
0.909 (1.00) |
0.0981 (1.00) |
0.688 (1.00) |
0.92 (1.00) |
0.949 (1.00) |
0.712 (1.00) |
0.773 (1.00) |
0.817 (1.00) |
|
8q gain | 0 (0%) | 489 |
0.77 (1.00) |
0.032 (1.00) |
0.509 (1.00) |
0.129 (1.00) |
0.592 (1.00) |
0.0956 (1.00) |
0.917 (1.00) |
0.3 (1.00) |
|
9p gain | 0 (0%) | 792 |
0.506 (1.00) |
0.539 (1.00) |
1 (1.00) |
0.235 (1.00) |
0.536 (1.00) |
0.143 (1.00) |
0.284 (1.00) |
0.0222 (1.00) |
|
9q gain | 0 (0%) | 803 |
0.432 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.143 (1.00) |
1 (1.00) |
0.211 (1.00) |
0.434 (1.00) |
0.0693 (1.00) |
|
10p gain | 0 (0%) | 751 |
0.778 (1.00) |
0.838 (1.00) |
0.611 (1.00) |
0.279 (1.00) |
0.525 (1.00) |
0.664 (1.00) |
0.113 (1.00) |
0.00129 (0.818) |
|
10q gain | 0 (0%) | 813 |
0.791 (1.00) |
0.347 (1.00) |
1 (1.00) |
0.282 (1.00) |
0.867 (1.00) |
0.983 (1.00) |
0.919 (1.00) |
0.0575 (1.00) |
|
11q gain | 0 (0%) | 812 |
0.0481 (1.00) |
0.848 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.883 (1.00) |
0.093 (1.00) |
0.998 (1.00) |
0.967 (1.00) |
|
12p gain | 0 (0%) | 745 |
0.765 (1.00) |
0.562 (1.00) |
0.0206 (1.00) |
0.24 (1.00) |
0.132 (1.00) |
0.614 (1.00) |
0.788 (1.00) |
0.574 (1.00) |
|
12q gain | 0 (0%) | 772 |
0.156 (1.00) |
0.198 (1.00) |
0.0509 (1.00) |
0.291 (1.00) |
0.0456 (1.00) |
0.744 (1.00) |
0.866 (1.00) |
0.572 (1.00) |
|
13q gain | 0 (0%) | 812 |
0.825 (1.00) |
0.988 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.0878 (1.00) |
0.326 (1.00) |
0.0681 (1.00) |
0.526 (1.00) |
|
15q gain | 0 (0%) | 813 |
0.652 (1.00) |
0.625 (1.00) |
0.379 (1.00) |
0.152 (1.00) |
0.757 (1.00) |
0.98 (1.00) |
0.613 (1.00) |
0.793 (1.00) |
|
16p gain | 0 (0%) | 612 |
0.626 (1.00) |
0.0278 (1.00) |
1 (1.00) |
0.19 (1.00) |
0.502 (1.00) |
0.0781 (1.00) |
0.0821 (1.00) |
0.0568 (1.00) |
|
16q gain | 0 (0%) | 804 |
0.177 (1.00) |
0.773 (1.00) |
0.439 (1.00) |
0.87 (1.00) |
0.0906 (1.00) |
0.53 (1.00) |
0.992 (1.00) |
0.962 (1.00) |
|
17p gain | 0 (0%) | 811 |
0.667 (1.00) |
0.483 (1.00) |
0.00969 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.419 (1.00) |
0.388 (1.00) |
0.565 (1.00) |
|
17q gain | 0 (0%) | 737 |
0.805 (1.00) |
0.655 (1.00) |
0.0262 (1.00) |
0.82 (1.00) |
0.108 (1.00) |
0.362 (1.00) |
0.58 (1.00) |
0.0198 (1.00) |
|
18p gain | 0 (0%) | 774 |
0.0989 (1.00) |
0.0335 (1.00) |
0.602 (1.00) |
0.06 (1.00) |
0.458 (1.00) |
0.478 (1.00) |
0.685 (1.00) |
0.109 (1.00) |
|
18q gain | 0 (0%) | 783 |
0.132 (1.00) |
0.578 (1.00) |
0.558 (1.00) |
0.204 (1.00) |
0.359 (1.00) |
0.914 (1.00) |
0.905 (1.00) |
0.139 (1.00) |
|
19p gain | 0 (0%) | 789 |
0.0603 (1.00) |
0.211 (1.00) |
0.156 (1.00) |
0.143 (1.00) |
0.232 (1.00) |
0.641 (1.00) |
0.349 (1.00) |
0.614 (1.00) |
|
19q gain | 0 (0%) | 773 |
0.00779 (1.00) |
0.811 (1.00) |
0.218 (1.00) |
0.424 (1.00) |
0.0228 (1.00) |
0.159 (1.00) |
0.313 (1.00) |
0.199 (1.00) |
|
20p gain | 0 (0%) | 624 |
0.0457 (1.00) |
0.107 (1.00) |
0.067 (1.00) |
0.859 (1.00) |
0.44 (1.00) |
0.475 (1.00) |
0.026 (1.00) |
0.932 (1.00) |
|
20q gain | 0 (0%) | 589 |
0.141 (1.00) |
0.484 (1.00) |
0.148 (1.00) |
0.67 (1.00) |
0.492 (1.00) |
0.333 (1.00) |
0.0158 (1.00) |
0.669 (1.00) |
|
21q gain | 0 (0%) | 758 |
0.0436 (1.00) |
0.0269 (1.00) |
1 (1.00) |
0.0252 (1.00) |
0.407 (1.00) |
0.78 (1.00) |
0.0254 (1.00) |
0.182 (1.00) |
|
22q gain | 0 (0%) | 817 |
0.808 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.0559 (1.00) |
0.725 (1.00) |
0.247 (1.00) |
|
Xq gain | 0 (0%) | 837 |
0.118 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.00936 (1.00) |
0.604 (1.00) |
0.953 (1.00) |
|
1p loss | 0 (0%) | 741 |
0.14 (1.00) |
0.00937 (1.00) |
1 (1.00) |
0.42 (1.00) |
0.881 (1.00) |
0.0136 (1.00) |
0.0687 (1.00) |
0.0486 (1.00) |
|
1q loss | 0 (0%) | 836 |
0.627 (1.00) |
0.698 (1.00) |
1 (1.00) |
1 (1.00) |
0.784 (1.00) |
0.942 (1.00) |
0.625 (1.00) |
0.993 (1.00) |
|
2p loss | 0 (0%) | 784 |
0.826 (1.00) |
0.458 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.056 (1.00) |
0.675 (1.00) |
0.398 (1.00) |
0.11 (1.00) |
|
2q loss | 0 (0%) | 770 |
0.642 (1.00) |
0.674 (1.00) |
0.61 (1.00) |
0.24 (1.00) |
0.133 (1.00) |
0.457 (1.00) |
0.362 (1.00) |
0.052 (1.00) |
|
3p loss | 0 (0%) | 769 |
0.0356 (1.00) |
0.0497 (1.00) |
0.609 (1.00) |
0.434 (1.00) |
0.374 (1.00) |
0.998 (1.00) |
0.453 (1.00) |
0.787 (1.00) |
|
3q loss | 0 (0%) | 814 |
0.231 (1.00) |
0.0868 (1.00) |
1 (1.00) |
0.068 (1.00) |
0.125 (1.00) |
0.681 (1.00) |
0.699 (1.00) |
0.0809 (1.00) |
|
4p loss | 0 (0%) | 679 |
0.45 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.89 (1.00) |
0.466 (1.00) |
0.53 (1.00) |
0.439 (1.00) |
|
4q loss | 0 (0%) | 707 |
0.477 (1.00) |
0.966 (1.00) |
0.373 (1.00) |
0.466 (1.00) |
0.916 (1.00) |
0.288 (1.00) |
0.938 (1.00) |
0.435 (1.00) |
|
5p loss | 0 (0%) | 789 |
0.139 (1.00) |
0.106 (1.00) |
0.527 (1.00) |
0.884 (1.00) |
0.419 (1.00) |
0.949 (1.00) |
0.818 (1.00) |
0.671 (1.00) |
|
5q loss | 0 (0%) | 738 |
0.306 (1.00) |
0.118 (1.00) |
0.621 (1.00) |
0.647 (1.00) |
0.958 (1.00) |
0.385 (1.00) |
0.206 (1.00) |
0.277 (1.00) |
|
6p loss | 0 (0%) | 748 |
0.254 (1.00) |
0.128 (1.00) |
0.613 (1.00) |
0.343 (1.00) |
0.118 (1.00) |
0.844 (1.00) |
0.942 (1.00) |
0.836 (1.00) |
|
6q loss | 0 (0%) | 691 |
0.952 (1.00) |
0.00697 (1.00) |
0.219 (1.00) |
0.133 (1.00) |
0.3 (1.00) |
0.984 (1.00) |
0.644 (1.00) |
0.778 (1.00) |
|
7p loss | 0 (0%) | 810 |
0.526 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.296 (1.00) |
0.888 (1.00) |
0.643 (1.00) |
0.582 (1.00) |
0.0371 (1.00) |
|
7q loss | 0 (0%) | 794 |
0.132 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.206 (1.00) |
0.75 (1.00) |
0.301 (1.00) |
0.0349 (1.00) |
|
8p loss | 0 (0%) | 600 |
0.00387 (1.00) |
0.538 (1.00) |
1 (1.00) |
0.863 (1.00) |
0.496 (1.00) |
0.21 (1.00) |
0.176 (1.00) |
0.807 (1.00) |
|
8q loss | 0 (0%) | 812 |
0.00592 (1.00) |
0.931 (1.00) |
1 (1.00) |
0.594 (1.00) |
0.336 (1.00) |
0.602 (1.00) |
0.424 (1.00) |
0.635 (1.00) |
|
9p loss | 0 (0%) | 673 |
0.0158 (1.00) |
0.958 (1.00) |
0.413 (1.00) |
0.441 (1.00) |
0.63 (1.00) |
0.377 (1.00) |
0.675 (1.00) |
0.295 (1.00) |
|
9q loss | 0 (0%) | 717 |
0.0163 (1.00) |
0.539 (1.00) |
0.17 (1.00) |
0.915 (1.00) |
0.277 (1.00) |
0.304 (1.00) |
0.994 (1.00) |
0.344 (1.00) |
|
10p loss | 0 (0%) | 785 |
0.0778 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.0687 (1.00) |
0.439 (1.00) |
0.496 (1.00) |
0.356 (1.00) |
|
10q loss | 0 (0%) | 751 |
0.00376 (1.00) |
0.692 (1.00) |
0.611 (1.00) |
0.473 (1.00) |
0.356 (1.00) |
0.31 (1.00) |
0.737 (1.00) |
0.38 (1.00) |
|
11p loss | 0 (0%) | 719 |
0.0149 (1.00) |
0.383 (1.00) |
0.369 (1.00) |
0.59 (1.00) |
0.934 (1.00) |
0.934 (1.00) |
0.0374 (1.00) |
0.333 (1.00) |
|
11q loss | 0 (0%) | 637 |
0.156 (1.00) |
0.617 (1.00) |
0.0534 (1.00) |
0.469 (1.00) |
0.398 (1.00) |
0.714 (1.00) |
0.151 (1.00) |
0.036 (1.00) |
|
12p loss | 0 (0%) | 792 |
0.0972 (1.00) |
0.995 (1.00) |
0.51 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.45 (1.00) |
0.866 (1.00) |
0.764 (1.00) |
|
12q loss | 0 (0%) | 807 |
0.229 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.786 (1.00) |
0.82 (1.00) |
0.604 (1.00) |
0.418 (1.00) |
|
13q loss | 0 (0%) | 600 |
0.0791 (1.00) |
0.176 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.39 (1.00) |
0.0928 (1.00) |
0.613 (1.00) |
0.921 (1.00) |
|
14q loss | 0 (0%) | 730 |
0.00846 (1.00) |
0.217 (1.00) |
0.37 (1.00) |
1 (1.00) |
0.585 (1.00) |
0.444 (1.00) |
0.862 (1.00) |
0.812 (1.00) |
|
15q loss | 0 (0%) | 701 |
0.234 (1.00) |
0.174 (1.00) |
0.377 (1.00) |
0.475 (1.00) |
0.246 (1.00) |
0.872 (1.00) |
0.452 (1.00) |
0.267 (1.00) |
|
16p loss | 0 (0%) | 804 |
0.962 (1.00) |
0.657 (1.00) |
0.102 (1.00) |
0.87 (1.00) |
0.471 (1.00) |
0.552 (1.00) |
0.435 (1.00) |
0.408 (1.00) |
|
16q loss | 0 (0%) | 491 |
0.0272 (1.00) |
0.00135 (0.852) |
1 (1.00) |
0.473 (1.00) |
0.638 (1.00) |
0.792 (1.00) |
0.0564 (1.00) |
0.928 (1.00) |
|
17p loss | 0 (0%) | 500 |
0.338 (1.00) |
0.0245 (1.00) |
0.742 (1.00) |
0.0773 (1.00) |
0.544 (1.00) |
0.383 (1.00) |
0.331 (1.00) |
0.502 (1.00) |
|
17q loss | 0 (0%) | 720 |
0.598 (1.00) |
0.238 (1.00) |
0.368 (1.00) |
0.914 (1.00) |
0.934 (1.00) |
0.659 (1.00) |
0.213 (1.00) |
0.872 (1.00) |
|
18p loss | 0 (0%) | 690 |
0.00592 (1.00) |
0.00127 (0.804) |
1 (1.00) |
0.425 (1.00) |
0.593 (1.00) |
0.681 (1.00) |
0.27 (1.00) |
0.445 (1.00) |
|
18q loss | 0 (0%) | 691 |
0.0396 (1.00) |
0.00111 (0.707) |
1 (1.00) |
0.483 (1.00) |
0.292 (1.00) |
0.581 (1.00) |
0.149 (1.00) |
0.0271 (1.00) |
|
19p loss | 0 (0%) | 791 |
0.533 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.194 (1.00) |
0.0903 (1.00) |
0.538 (1.00) |
0.231 (1.00) |
|
19q loss | 0 (0%) | 805 |
0.632 (1.00) |
0.991 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.724 (1.00) |
0.0377 (1.00) |
0.846 (1.00) |
0.0419 (1.00) |
|
20p loss | 0 (0%) | 807 |
0.00351 (1.00) |
0.944 (1.00) |
0.419 (1.00) |
0.866 (1.00) |
0.537 (1.00) |
0.223 (1.00) |
0.317 (1.00) |
0.475 (1.00) |
|
20q loss | 0 (0%) | 830 |
0.576 (1.00) |
0.865 (1.00) |
1 (1.00) |
0.65 (1.00) |
0.277 (1.00) |
0.57 (1.00) |
0.754 (1.00) |
0.679 (1.00) |
|
21q loss | 0 (0%) | 774 |
0.961 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.0863 (1.00) |
0.728 (1.00) |
0.459 (1.00) |
0.0257 (1.00) |
|
22q loss | 0 (0%) | 569 |
0.124 (1.00) |
0.845 (1.00) |
0.172 (1.00) |
0.111 (1.00) |
0.41 (1.00) |
0.0533 (1.00) |
0.097 (1.00) |
0.48 (1.00) |
|
Xq loss | 0 (0%) | 826 |
0.0537 (1.00) |
0.722 (1.00) |
0.0389 (1.00) |
0.297 (1.00) |
0.578 (1.00) |
0.931 (1.00) |
0.377 (1.00) |
0.791 (1.00) |
P value = 3.84e-12 (Chi-square test), Q value = 2.5e-09
Table S1. Gene #8: '4q gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 8 | 246 | 165 | 2 | 107 | 22 | 36 | 9 | 12 |
4Q GAIN CNV | 3 | 0 | 2 | 0 | 9 | 2 | 0 | 1 | 3 | 2 | 1 | 0 |
4Q GAIN WILD-TYPE | 68 | 45 | 0 | 8 | 237 | 163 | 2 | 106 | 19 | 34 | 8 | 12 |
Figure S1. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
![](D8V9.png)
P value = 0.000337 (Chi-square test), Q value = 0.21
Table S2. Gene #21: '11p gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 8 | 246 | 165 | 2 | 107 | 22 | 36 | 9 | 12 |
11P GAIN CNV | 4 | 4 | 2 | 0 | 26 | 8 | 0 | 10 | 0 | 1 | 0 | 1 |
11P GAIN WILD-TYPE | 67 | 41 | 0 | 8 | 220 | 157 | 2 | 97 | 22 | 35 | 9 | 11 |
Figure S2. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
![](D21V9.png)
P value = 7.8e-05 (Chi-square test), Q value = 0.05
Table S3. Gene #26: '14q gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 71 | 45 | 2 | 8 | 246 | 165 | 2 | 107 | 22 | 36 | 9 | 12 |
14Q GAIN CNV | 3 | 1 | 2 | 0 | 23 | 11 | 1 | 15 | 1 | 5 | 0 | 2 |
14Q GAIN WILD-TYPE | 68 | 44 | 0 | 8 | 223 | 154 | 1 | 92 | 21 | 31 | 9 | 10 |
Figure S3. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'
![](D26V9.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = BRCA-TP.clin.merged.picked.txt
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Number of patients = 857
-
Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 9
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.